Mon Oct 10 13:58:40 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:58:40 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6480976 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -15.45400 39.47600 ymin,ymax (A): -25.95200 22.74400 zmin,zma (A): -7.346000 36.21800 x,y,z range (A): 54.93000 48.69600 43.56400 scale (grids/A): 0.6480976 object centre (A): 12.01100 -1.604000 14.43600 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999971 assigned positive charge : 324.0238 centred at (gu) : 89.08777 90.86368 88.90366 assigned negative charge : -331.0240 centred at (gu) : 89.34830 90.94633 88.95335 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5993 nv = 96 ne = 84 npr = 44072 no. pairs analyzed = 44072 no. exposed pairs = 2782 no. arc points = 19526 no. surface atoms = 935 nbur = 1213 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 282 mr = 3150 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2700000 number of dielectric boundary points 3111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1929 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7145 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5962641E-09 -1.5314020E-08 midg,1,midg; midg,igrid,midg -2.5400864E-09 -2.7990039E-08 1,midg,midg; igrid,midg,midg 2.2383203E-08 -3.8025568E-08 gauss-seidel spectral radius is 0.9876227 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 13:58:41 rms-change max change #iterations 0.1421668 22.50326 at 10iterations 1.4449185E-02 2.178707 at 20iterations 1.4561178E-03 0.2402458 at 30iterations 1.4454059E-04 2.3994446E-02 at 40iterations 1.4997418E-05 2.6531219E-03 at 50iterations finished qdiffx linear iterations at : 13:58:43 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.4997418E-05 2.6531219E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 13:58:44 3.375u 0.186s 0:04.05 87.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:58:44 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.944293 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -15.45400 39.47600 ymin,ymax (A): -25.95200 22.74400 zmin,zma (A): -7.346000 36.21800 x,y,z range (A): 54.93000 48.69600 43.56400 scale (grids/A): 1.944293 object centre (A): 12.01100 -1.604000 14.43600 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999971 assigned positive charge : 324.0238 centred at (gu) : 87.26310 92.59107 86.71081 assigned negative charge : -331.0240 centred at (gu) : 88.04502 92.83900 86.85989 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 64057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19526 grid for indexing accessible points = 1.400000 m= 22637 mr = 43236 m= 3451 mr = 16324 m= 174 mr = 2037 m= 4 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 412 time to turn everything in is 0.5700000 number of dielectric boundary points 28687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15812 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6480976 object centre at (A) : 12.01100 -1.604000 14.43600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5279921E-03 -1.7505510E-02 midg,1,midg; midg,igrid,midg -3.3359122E-03 -1.5319312E-02 1,midg,midg; igrid,midg,midg 2.9747408E-02 -7.3487125E-02 gauss-seidel spectral radius is 0.9986409 estimated iterations to convergence 215 setup time was (sec) 0.8800000 now iterating at: 13:58:45 rms-change max change #iterations 4.028951 235.5309 at 10iterations 1.887889 67.70998 at 20iterations 0.8843664 31.97491 at 30iterations 0.4128948 13.61732 at 40iterations 0.1952656 7.039412 at 50iterations 9.1308139E-02 3.067871 at 60iterations 4.2831160E-02 1.348208 at 70iterations 2.0090226E-02 0.6399546 at 80iterations 9.4037000E-03 0.3248310 at 90iterations 4.3985988E-03 0.1543021 at 100iterations 2.0673042E-03 6.8159103E-02 at 110iterations 9.6624537E-04 3.5236359E-02 at 120iterations finished qdiffx linear iterations at : 13:58:51 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 9.6624537E-04 3.5236359E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 13:58:52 7.467u 0.181s 0:08.28 92.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:58:52 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.916439 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -15.45400 39.47600 ymin,ymax (A): -25.95200 22.74400 zmin,zma (A): -7.346000 36.21800 x,y,z range (A): 54.93000 48.69600 43.56400 scale (grids/A): 2.916439 object centre (A): 12.01100 -1.604000 14.43600 number of atom coordinates read : 2148 total number of charged atoms : 2007 net assigned charge : -6.999971 assigned positive charge : 324.0238 centred at (gu) : 85.89468 93.88666 85.06625 assigned negative charge : -331.0240 centred at (gu) : 87.06757 94.25851 85.28982 start vw surface at 0.2000000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 148000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19526 grid for indexing accessible points = 1.400000 m= 73046 mr = 104988 m= 26256 mr = 58934 m= 6051 mr = 20814 m= 738 mr = 4352 m= 27 mr = 421 m= 0 mr = 6 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 1537 time to turn everything in is 1.270000 number of dielectric boundary points 64603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 16055 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.944293 object centre at (A) : 12.01100 -1.604000 14.43600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1771860E-02 -0.1752160 midg,1,midg; midg,igrid,midg -7.4362397E-02 -8.3670191E-02 1,midg,midg; igrid,midg,midg 0.3256782 -0.7394101 gauss-seidel spectral radius is 0.9992508 estimated iterations to convergence 288 setup time was (sec) 1.560000 now iterating at: 13:58:54 rms-change max change #iterations 9.429914 344.5215 at 10iterations 5.449835 128.9376 at 20iterations 3.155098 63.70128 at 30iterations 1.813905 37.07702 at 40iterations 1.042868 21.35073 at 50iterations 0.5978769 13.00023 at 60iterations 0.3433117 6.854949 at 70iterations 0.1966154 4.077719 at 80iterations 0.1126988 2.331120 at 90iterations 6.4622961E-02 1.335728 at 100iterations 3.6938280E-02 0.6850758 at 110iterations 2.1143790E-02 0.3911114 at 120iterations 1.2106294E-02 0.2291050 at 130iterations 6.9161002E-03 0.1384850 at 140iterations 3.9633955E-03 7.5265408E-02 at 150iterations 2.2653495E-03 4.2129517E-02 at 160iterations 1.2954051E-03 2.6880264E-02 at 170iterations 7.4214290E-04 1.4085770E-02 at 180iterations finished qdiffx linear iterations at : 13:59:04 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 7.4214290E-04 1.4085770E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 13:59:05 11.875u 0.192s 0:12.39 97.3% 0+0k 0+0io 0pf+0w